I am analyzing Hi-C data with HOMER. My experimental set up is time-point wise analysis of stress (0,1 and 6 hrs). For a differential analysis, say 6 hrs vs 0 hr, how can I find interactions which are over-represented, under_represented and specific to only one condition ? I had initially just used the FDR values to fish out significant interactions. There is a confusion in my lab regarding this issue and we are stuck at a critical point. Kindly help.
I have the following important columns in the interaction table for 6 hrs vs 0 hr: